Functional assignment of Mycobacterium tuberculosis proteome revealed by genome-scale fold-recognition

Tuberculosis

Volumn 93, Issue 1, 2013, Pages 40-46

  Mao, Chunhong ^a   Shukla, Maulik ^a   Larrouy Maumus, Gérald ^b   Dix, Flora L ^b   Kelley, Lawrence A ^c   Sternberg, Michael J ^c   Sobral, Bruno W ^a,d   De Carvalho, Luiz Pedro S ^b  

^a VIRGINIA BIOINFORMATICS INSTITUTE   (United States)

^b NATIONAL INSTITUTE FOR MEDICAL RESEARCH   (United Kingdom)

^c IMPERIAL COLLEGE LONDON   (United Kingdom)

^d NESTLÉ RESEARCH CENTER   (Switzerland)

Author keywords

Enzymatic activity; Fold recognition; Functional genomics; Mycobacterium tuberculosis; Phyre2; Protein function

Indexed keywords

PROTEOME;

AMINO ACID SEQUENCE; BIOINFORMATICS; ENZYME SPECIFICITY; GENETIC CODE; GENOME; GENOMICS; MYCOBACTERIUM TUBERCULOSIS; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN FUNCTION; REVIEW; SEQUENCE HOMOLOGY; TUBERCULOSIS;

BACTERIAL PROTEINS; COMPUTATIONAL BIOLOGY; GENOME, BACTERIAL; HUMANS; MODELS, MOLECULAR; MYCOBACTERIUM TUBERCULOSIS; PROTEIN FOLDING; PROTEOME;

EID: 84874548906     PISSN: 14729792     EISSN: 1873281X     Source Type: Journal    
DOI: 10.1016/j.tube.2012.11.008     Document Type: Review

References (20)

1. A. Pawlowski, M. Jansson, M. Skold, M.E. Rottenberg, and G. Kallenius Tuberculosis and HIV co-infection PLoS Pathog 8 2012 e1002464 doi:10.1371/journal.ppat. 1002464PPATHOGENS-D-11-01902 [pii]
2. E.L. Corbett, C.J. Watt, N. Walker, D. Maher, B.G. Williams, M.C. Raviglione, and C. Dye The growing burden of tuberculosis: global trends and interactions with the HIV epidemic Arch Intern Med 163 2003 1009 1021 doi:10.1001/archinte.163.9.1009163/9/1009 [pii]
3. H. Getahun, C. Gunneberg, R. Granich, and P. Nunn HIV infection-associated tuberculosis: the epidemiology and the response Clin Infect Dis 50 Suppl. 3 2010 S201 S207 10.1086/651492
4. M.A. Espinal, and M. Salfinger Stewart T. Cole, Kathleen Dd. Eisenach, David N. McMurray, William R. Jacobs Jr. Tuberculosis and the tubercle bacillus 2005 ASM Press 101 114
5. S.T. Cole, R. Brosch, J. Parkhill, T. Garnier, C. Churcher, D. Harris, S.V. Gordon, K. Eiglmeier, S. Gas, C.E. Barry 3rd, F. Tekaia, K. Badcock, D. Basham, D. Brown, T. Chillingworth, R. Connor, R. Davies, K. Devlin, T. Feltwell, S. Gentles, N. Hamlin, S. Holroyd, T. Hornsby, K. Jagels, A. Krogh, J. McLean, S. Moule, L. Murphy, K. Oliver, J. Osborne, M.A. Quail, M.A. Rajandream, J. Rogers, S. Rutter, K. Seeger, J. Skelton, R. Squares, S. Squares, J.E. Sulston, K. Taylor, S. Whitehead, and B.G. Barrell Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence Nature 393 1998 537 544 10.1038/31159
6. J.C. Camus, M.J. Pryor, C. Medigue, and S.T. Cole Re-annotation of the genome sequence of Mycobacterium tuberculosis H37Rv Microbiology 148 2002 2967 2973
7. J.M. Lew, A. Kapopoulou, L.M. Jones, and S.T. Cole TubercuList-10 years after Tuberculosis (Edinb) 91 2011 1 7 doi:S1472-9792(10)00111-3 [pii]10.1016/j.tube.2010.09.008
8. A. Argyrou, and J.S. Blanchard Mycobacterium tuberculosis lipoamide dehydrogenase is encoded by Rv0462 and not by the lpdA or lpdB genes Biochemistry 40 2001 11353 11363 doi:bi010575o [pii]
9. T. Doerks, V. van Noort, P. Minguez, and P. Bork Annotation of the M. tuberculosis hypothetical orfeome: adding functional information to more than half of the uncharacterized proteins PLoS One 7 2012 e34302 doi:10.1371/journal. pone.0034302PONE-D-11-24795 [pii]
10. J. Muller, D. Szklarczyk, P. Julien, I. Letunic, A. Roth, M. Kuhn, S. Powell, C. von Mering, T. Doerks, L.J. Jensen, and P. Bork eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations Nucleic Acids Res 38 2010 D190 D195 doi:gkp951 [pii] 10.1093/nar/gkp951
11. D. Szklarczyk, A. Franceschini, M. Kuhn, M. Simonovic, A. Roth, P. Minguez, T. Doerks, M. Stark, J. Muller, P. Bork, L.J. Jensen, and C. von Mering The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored Nucleic Acids Res 39 2011 D561 D568 doi:gkq973 [pii] 10.1093/nar/gkq973
12. G.K. Mazandu, and N.J. Mulder Function prediction and analysis of Mycobacterium tuberculosis hypothetical proteins Int J Mol Sci 13 2012 7283 7302 doi:10.3390/ijms13067283 ijms-13-07283 [pii]
13. G.K. Mazandu, and N.J. Mulder Using the underlying biological organization of the Mycobacterium tuberculosis functional network for protein function prediction Infect Genet Evol 12 2012 922 932 doi:S1567-1348(11)00385-6 [pii]10.1016/j.meegid.2011.10.027
14. R.M. Bennett-Lovsey, A.D. Herbert, M.J. Sternberg, and L.A. Kelley Exploring the extremes of sequence/structure space with ensemble fold recognition in the program Phyre Proteins 70 2008 611 625 10.1002/prot.21688
15. L.A. Kelley, and M.J. Sternberg Protein structure prediction on the Web: a case study using the Phyre server Nat Protoc 4 2009 363 371 doi:nprot.2009.2 [pii] 10.1038/nprot.2009.2
16. J.J. Gillespie, A.R. Wattam, S.A. Cammer, J.L. Gabbard, M.P. Shukla, O. Dalay, T. Driscoll, D. Hix, S.P. Mane, C. Mao, E.K. Nordberg, M. Scott, J.R. Schulman, E.E. Snyder, D.E. Sullivan, C. Wang, A. Warren, K.P. Williams, T. Xue, H.S. Yoo, C. Zhang, Y. Zhang, R. Will, R.W. Kenyon, and B.W. Sobral PATRIC: the comprehensive bacterial bioinformatics resource with a focus on human pathogenic species Infect Immun 79 2011 4286 4298 doi:IAI.00207-11 [pii] 10.1128/IAI.00207-11
17. R.K. Aziz, D. Bartels, A.A. Best, M. DeJongh, T. Disz, R.A. Edwards, K. Formsma, S. Gerdes, E.M. Glass, M. Kubal, F. Meyer, G.J. Olsen, R. Olson, A.L. Osterman, R.A. Overbeek, L.K. McNeil, D. Paarmann, T. Paczian, B. Parrello, G.D. Pusch, C. Reich, R. Stevens, O. Vassieva, V. Vonstein, A. Wilke, and O. Zagnitko The RAST server: rapid annotations using subsystems technology BMC Genomics 9 2008 75 doi:1471-2164-9-75 [pii] 10.1186/1471-2164-9-75
18. D.L. Purich Advances in the enzymology of glutamine synthesis Adv Enzymol Relat Areas Mol Biol 72 1998 9 42
19. M.J. van der Werf, K.M. Overkamp, and J.A. de Bont Limonene-1,2-epoxide hydrolase from Rhodococcus erythropolis DCL14 belongs to a novel class of epoxide hydrolases J Bacteriol 180 1998 5052 5057
20. E.G. Ahuja, P. Janning, M. Mentel, A. Graebsch, R. Breinbauer, W. Hiller, B. Costisella, L.S. Thomashow, D.V. Mavrodi, and W. Blankenfeldt PhzA/B catalyzes the formation of the tricycle in phenazine biosynthesis J Am Chem Soc 130 2008 17053 17061 10.1021/ja806325k